From 4a4f1560c4784bfe8f84668997900dacb6cfa4c3 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 19 Apr 2011 02:48:19 +0000 Subject: [PATCH] in progress --- forester/java/src/org/forester/archaeopteryx/TreePanel.java | 11 +++++++++++ .../org/forester/archaeopteryx/UniProtSequenceObtainer.java | 6 ++++++ 2 files changed, 17 insertions(+) diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index c01fb48..e1bcfb7 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -3344,6 +3344,17 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( node ).length() > 0 ) ) { x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " ); } + if ( getControlPanel().isShowGeneNames() ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " ); + } + if ( getControlPanel().isShowGeneSymbols() ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " ); + } + if ( getControlPanel().isShowSequenceAcc() ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession() + .toString() + + " " ); + } if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) { x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " ); } diff --git a/forester/java/src/org/forester/archaeopteryx/UniProtSequenceObtainer.java b/forester/java/src/org/forester/archaeopteryx/UniProtSequenceObtainer.java index 4751335..fa5ae63 100644 --- a/forester/java/src/org/forester/archaeopteryx/UniProtSequenceObtainer.java +++ b/forester/java/src/org/forester/archaeopteryx/UniProtSequenceObtainer.java @@ -154,6 +154,12 @@ public class UniProtSequenceObtainer implements Runnable { if ( query.indexOf( '/' ) > 0 ) { query = query.substring( 0, query.indexOf( '/' ) ); } + if ( query.indexOf( '.' ) > 0 ) { + query = query.substring( 0, query.indexOf( '.' ) ); + } + if ( query.indexOf( '_' ) > 0 ) { + query = query.substring( 0, query.indexOf( '_' ) ); + } final UniProtEntry upe = obtainUniProtEntry( query ); if ( upe != null ) { final Sequence seq = new Sequence(); -- 1.7.10.2